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C&EN’s writers and editors selected the finalists on the strength of their groundbreaking chemistry from nominations that readers and advisers sent from far and wide.

The scientists behind this year’s class aim to change how the world treats disease, stores energy, grows food, and produces a range of chemicals and materials. Their 10 companies represent the breadth of the chemical enterprise and the many ways chemists are working to solve some of society’s most pressing problems.

Some of those problems are better known than others. For example, Ionic Materials wants to prevent the high-profile problem of lithium-ion batteries catching fire and causing accidents. In contrast, few may be familiar with Solugen’s target: the cost and waste involved in producing hydrogen peroxide.

Start-ups’ solutions can hinge on brand-new science. Kymera Therapeutics is finding entirely new drug targets to attack with protein degradation. Kronos Bio has raised funds to pursue a class of proteins called transcription factors using research that hasn’t even been published.

Other start-ups are pushing existing technologies to the next level—opening up the world’s fungi to genome mining, bringing color and video to low-energy reflective displays, and killing pests with RNA interference.

It is harder than ever to launch a venture-backed company, according to the National Venture Capital Association. It takes 3.7 years on average for start-ups to raise their first rounds of funds, about a year longer than in 2014.

Some firms have a bigger pool of funds to tap than others: In 2018, investment in pharma and biotech start-ups is expected to reach a record high of over $14 billion. And those that raise that first round of funds will find that corporate investors are becoming more prominent.

We’re sure that the stories to follow won’t be the last you’ll hear about these 10 companies. If you know an exceptional new company with chemistry at its core, nominate it for next year’s feature at cenm.ag/startupnom.

Bodle Technologies

Creating low-energy reflective displays—with color and video

Cofounders Peiman Hosseini (left) and Harish Bhaskaran with an early prototype of a solid-state reflective display

At a glance

Launched: 2015

Headquarters: Oxford, England

Focus: Reflective display screen with color and video

Technology: Phase-change materials

Founders: ﻿Harish Bhaskaran, David Fyfe, and Peiman Hosseini

Funding or notable partner: University of Oxford

Bodle Technologies, spun off in 2015 from the University of Oxford, is hoping to revolutionize electronic screens with its solid-state reflective displays (SRDs).

SRDs use very little energy and provide high contrast even in low light, which is why they are used in e-book readers. But critically, the displays lack color and video capability; despite their best efforts, Amazon and other major manufacturers have been flummoxed in their efforts to move SRD technology to the next level.

With a research budget a fraction of that thrown at the challenge by a host of global technology corporations, Bodle is a front-runner in the race to roll out a commercial color product. In tests, its SRD provides the sharpest and most colorful images among all technologies in development, the company claims.

Credit: Bodle Technologies/C&EN

Bodle's displays contain phase-change materials that feature optical cavities designed to reflect targeted colors of light, shown as colored arrows. A pulse of electricity flips the phase-change material from a crystalline to an amorphous state. This causes a modification to the optical cavities, leading to a change in the material's refractive index, which causes a shift in the color of the reflected light. An additional electric pulse reverses the process.

Key to Bodle’s technology are pixels made from phase-change alloys featuring optical nanocavities that can be switched back and forth from amorphous to crystalline when hit with an electrical impulse. The switch causes individual pixels to change color; maintaining that color requires no further power.

The alloys feature elements such as germanium, antimony, and tellurium. Bodle has developed green, blue, and red pixels that can be combined to cover the whole color spectrum.

“The beauty of our technology is in its simplicity,” says Richard Holliday, Bodle’s head of business development and intellectual property. “There are no moving parts, organic materials, or
liquids.”

Bodle’s headquarters—a 400-year-old former stable in a science park just outside Oxford, England—are not an obvious place for a display technology firm; these companies tend to be in modern settings in Asia or the U.S. Even the company’s name has an ancient source: It is taken from the Bodleian Library, the University of Oxford’s main research library, which opened its doors to scholars in 1602.

But the science park hosts shared facilities, including a clean room and a laser instrument for testing pixel materials. And the location is close to the university, which provides ongoing support. Indeed, Harish Bhaskaran, professor of applied nanomaterials at Oxford and Bodle’s cofounder and chief scientific officer, is just minutes down the road. The firm has had no trouble attracting prospective customers to the leafy site, Holliday adds.

Neither has the company struggled to raise funds. Bodle secured $3.7 million in seed funding in 2015–16, led by the university’s technology investment arm, Oxford Sciences Innovation. In January of this year it raised a further $8.5 million in series A funding from venture capital firms and the university.

“Other companies are developing competing technologies,” Holliday says, “but their color intensity is far lower, their luminance is far less than Bodle’s, and none can match the speed at which Bodle’s SRD pixels can switch, which is less than a millisecond.”

Amazon dismantled Liquavista, a technology arm that had been developing a reflective color display for a Kindle, earlier this year. Liquavista sought to modify the surface tension of liquids on a solid surface.

Meanwhile, Bodle and its team of 14 staffers are pushing toward commercialization. The firm recently unveiled a prototype screen measuring about 10 cm2. Bodle has also demonstrated at the pixel level that its technology will work for video.

The company is optimizing the materials it uses to make its pixels and integrating them with the requisite electronics. It plans to roll out a demonstration color-video screen in mid-2019 and its first commercial product in the next couple of years.

Initially, Bodle hopes to carve out niche markets, such as dynamic-pricing screens for retail shelves and low-energy-consumption screens for wearable devices. SRD could spell the end for the chore of regularly recharging smart watches, Holliday says.

Ultimately, though, Bodle could go after the cell phone and laptop markets. The company is already confident that the cost of making SRDs will be on par with the cost of making the liquid-crystal and organic light-emitting diode displays on the market today.

At a glance

Funding or notable partners: More than $5 million from DICand other investors

Checkerspot CEO and cofounder Charles Dimmler has set lofty goals for his algae-based start-up. Its single-cell organisms make oil that Checkerspot transforms into novel triglyceride building blocks. “Our vision is to be the most impactful 21st-century materials company,” he says.

Dimmler claims the time is right for the Berkeley, Calif.-based firm’s technology. “Customers are seeking deeper purpose when it comes to decisions about what brands to support and what to buy,” he says. Consumer product companies are taking note and demanding sustainable raw materials.

But Dimmler doesn’t intend to simply sell substitutes for petrochemicals already in use. “Instead, we are thinking about how we can create materials that perform better and aren’t simply swap-in, swap-out replacements,” he says.

Credit: C&EN

Checkerspot ferments microalgae to make tailored triglycerides. In one example, the microbes produce triolein, which is made into polyols for polyurethanes. These polyurethanes form the cores of lightweight surfboards.

Checkerspot ferments a class of sugar-eating microalgae, called trebouxiophyceae, which swell with fat. The company uses genetic engineering and classical strain improvement to coax the algae to produce useful triglycerides. It aims to create triglycerides built from fatty acids with customized chain lengths and positions of unsaturation, and even ones with functionality, such as hydroxyl groups, built in.

For example, Checkerspot is working with a major surfboard brand to develop a polyol based on triolein, a triglyceride made of three oleic acid chains. After fermenting microalgae and producing the triolein, Checkerspot generates the polyol by chemically attaching hydroxyl groups to the unsaturated bond at the ω-9 position on the oleic acids. The polyol is then reacted with isocyanates to make a polyurethane for a surfboard core that is light and stiff. Dimmler hopes to ride the surfboard wave into larger-volume applications such as automotive and aerospace.

Scott Franklin, cofounder and chief scientific officer, says the surfboard polyol application demonstrates an advantage of the firm’s approach. Commercially available vegetable oils contain a mixture of triglycerides, some of which are more useful to chemists than others. Checkerspot’s process can make the most useful triglycerides at high purity.

Polyols made from vegetable oil such as soybean oil, in contrast, contain unreactive unsaturated fatty acids. “They don’t participate in the chemistry, so they can detract from the physical properties that you are trying to get to,” Franklin says. The unreacted chains plasticize the polymer, making it rubbery, he notes.

The fatty acids in Checkerspot’s surfboard polyols, nearly 100% oleic, are all locked into the polymer structure. To make other polyols, Checkerspot can change the saturation and chain lengths of the fatty acids, Franklin says, customizing them for desired polymer properties.

In addition to the surfboard application, the company is working with the Swiss textile chemistry firm Beyond Surface Technologies on a water-repellent coating for outdoor apparel. The market, Dimmler says, is shifting away from fluorine-based chemistry. Checkerspot is also working on a specialty composite material for the skiing market.

Both Dimmler and Franklin are veterans of Solazyme, which once had big dreams of mass-producing algal-oil-based chemicals and biofuels. Solazyme renamed itself TerraVia in 2016 as it shifted focus to food ingredients. It declared bankruptcy a year later, and the Dutch firm Corbion scooped up its assets.

When it was founded in 2016, Checkerspot had the opportunity to license Solazyme technology, Dimmler says, but the new firm decided to start out with technology that it developed itself. He notes that Checkerspot’s business model is different. Solazyme aimed to build its own algae fermentation capacity at large scale to serve commodity markets. Checkerspot’s focus is on developing new specialty materials with partners and licensing the means to manufacture them.

Checkerspot signed one such agreement with Japan’s DIC to develop novel polyols. DIC, formerly named Dainippon Ink & Chemicals, has its own experience in algae. It has been making spirulina since the 1970s and now produces the algae-derived blue food coloring phycocyanin.

DIC also participated in a $5 million seed financing round along with KdT Ventures, which led the round, Viking Global Investors, and others. Another vote of confidence comes from Illumina Accelerator, which last year selected Checkerspot, along with four other firms, for its start-up program.

At a glance

Funding or notable partners: $20 million from investors, including 8VC

Not so long ago, scientists sought new drugs by gathering plants, dirt, or sea creatures, pulverizing them, testing the resulting broth in biological assays, and then figuring out which molecules in the mélange might be drug candidates. This “grind and bind” method of natural product discovery brought the world many blockbuster drugs, but it’s a slow process that’s fallen out of fashion.

The founders of Hexagon Bio think natural product drug discovery is due for a comeback. But they’re not searching for drugs in remote locations; instead, they’re mining the genomes of hard-to-culture microorganisms, particularly fungi.

As many as 5 million species of fungi grow on Earth, each of which may encode biosynthetic pathways for up to 80 different natural products. Growing fungi in the lab tends to take a long time, and fungi don’t express all their biosynthetic gene clusters actively. So eking out enough of those natural products to study—let alone commercialize—has been nearly impossible.

Credit: C&EN/Shutterstock

Scientists at Hexagon Bio mine fungal genomes using algorithms to find genes encoding biosynthetic pathways for natural products. They express these genes in yeast and test the natural products as drug candidates.

The scientists at Hexagon use a computer program to sift through genomic data from fungi and pluck out the genes that code for small-molecule biosynthetic pathways. They then insert those genes into a platform they developed—dubbed HEx, for heterologous expression—that coaxes engineered yeast to churn out proteins that biosynthesize natural products with possible therapeutic value.

“Instead of brewing alcohol, which a lot of people use yeast to do, we’re brewing medicines,” explains Maureen E. Hillenmeyer, Hexagon’s CEO and cofounder. “We’ve become experts at using yeast as a platform for producing chemicals that otherwise would be difficult or impossible to access.”

Hillenmeyer was working at the Stanford Genome Technology Center, part of Stanford University School of Medicine, when she and her colleagues invented the HEx platform. She was so enthusiastic about the technology that she decided to leave her position at Stanford to lead Hexagon Bio. It was clear to the company’s founders, she says, that they had discovered a way to capitalize on the past decade’s advances in DNA sequencing and synthesis. “For the whole natural products field in general, DNA sequencing is a big driver of change right now,” Hillenmeyer says. “Getting DNA is easy. Getting small molecules is hard.”

The first wave of genome-mining companies, with Warp Drive Bio the most prominent among them, sifted through bacterial genomes. Hexagon joins a cluster of biotechs examining fungi. What’s unique to Hexagon, Hillenmeyer notes, is its data-driven approach. To figure out which stretches of DNA make small molecules that could have potential as medicines, Hexagon invested significant time developing an algorithm that prioritizes, among the millions of possible gene clusters out there, which ones encode small molecules that specifically target human disease proteins.

“We, at the heart, are a data science company,” Hillenmeyer says. Hexagon’s location suggests that’s true: Its offices in Menlo Park, Calif., are a stone’s throw away from Facebook’s headquarters. Half the staff does computational work, while the other half focuses on experimental research.

With its computer algorithm and HEx platform in hand, Hexagon has the opportunity to access millions of compounds that have never been studied before. “These are compounds that have already gone through a form of combinatorial chemistry,” Hillenmeyer says. “Nature has already done the testing of millions of compounds and is serving us on a platter the ones that are exquisitely evolved to target proteins.”

Developing solid, nonflammable electrolytes for safer batteries

At a glance

Funding or notable partners: More than $65 million from investors, including Renault, Nissan, Mitsubishi, Hyundai, Kleiner Perkins, and Sun Microsystems cofounder Bill Joy﻿

Michael Zimmerman, CEO and founder of Ionic Materials, describes the liquid electrolyte in a typical lithium-ion battery as “a highway for electrons.” The trouble with the solvent-based electrolyte, he says, “is that it can explode like kerosene” when a short develops inside the battery.

Credit: Tufts University

Ionic Materials founder Michael Zimmerman is also a Tufts University faculty member.

Zimmerman claims to have found a way around that problem: a nonflammable polymeric electrolyte. Battery makers, he says, can easily and affordably drop his solid electrolyte into existing lithium-ion cells without making major design changes. Manufacturers will also be able to make batteries with greater energy densities for longer-lasting power for cars and electronics, he says.

Inspiration for the solid electrolyte came in 2011. At the time, consumers had become leery of lithium-ion batteries despite their ability to pack a lot of power in a small space for power-hungry portable electronics. In 2006, for instance, Dell recalled 4.1 million lithium-ion laptop batteries after several incidents in which they burst into flames. In 2010, a pallet of 81,000 lithium batteries self-ignited on a UPS cargo jet, causing the plane to crash.

Credit: C&EN/Shutterstock

In a typical lithium-ion battery, ions shuttle from the anode through a solvent-borne lithium salt electrolyte to a cathode. A separator film keeps the two electrodes from shorting. In Ionic Materials' solid-state battery, a solid crystalline polymer electrolyte serves a dual purpose: It is both an ion-conducting electrolyte and a separator film. Unlike the liquid electrolyte, the solid electrolyte is not flammable.

Zimmerman says the electrolyte replacement he developed is a nonflammable crystalline polymer that will not contribute fuel to a fire. Such an “inherently safe cell” can improve performance and reduce cost through simpler cooling and battery management systems than are possible with today’s lithium-ion cells, he says. To bring his concept to market, Zimmerman launched Ionic Materials in 2012.

He is reluctant to reveal specifics about the polymers and their characteristics for competitive reasons. However, patents he has filed on the solid electrolytes indicate they can be made from crystalline resins such as polyphenylene sulfide, polyphenylene oxide, polyether ether ketone, and polysulfone. Ionic Materials mixes the resins with ionic materials and dopants and then extrudes them into a film. The firm is now making small quantities of the film for testing.

In a typical lithium-ion battery, ions shuttle from a graphite anode through a solvent-borne lithium salt electrolyte to a
lithium-ion cathode. A separator film keeps the two electrodes from shorting. Ionic Materials’ solid electrolyte serves a dual purpose: It is both an ion-conducting electrolyte and a separator film.

Zimmerman readily admits he is not a battery scientist but says his perspective as an outsider helped him make his breakthrough. The holder of a Ph.D. in mechanical engineering and applied mechanics from the University of Pennsylvania, Zimmerman spent more than a decade at Bell Labs, where he worked on projects such as polymeric encapsulants for semiconductors and low-cost fiber-optic devices that connect to home networks.

For almost 30 years, Zimmerman has been a part-time faculty member at Tufts University School of Engineering. He also founded a liquid-crystal polymer packaging start-up that he has since sold. He says, “I developed the intellectual property for Ionic Materials working on my own the old-fashioned way: in my garage.”

Since starting up, Ionic Materials has attracted more than $65 million from strategic investors, such as the automakers Renault, Nissan, Mitsubishi, and Hyundai. The battery maker A123 Systems and the oil company Total, which owns the battery maker Saft, are investors too, as are the private equity firm Kleiner Perkins and Bill Joy, cofounder of Sun Microsystems.

Some of the funding will go to building a pilot line to make solid electrolytes. Polymer formulations for other high-performance batteries are in the works, including one that would make throwaway alkaline batteries rechargeable. “We are planning to become the solid-state battery materials firm of the future,” Zimmerman says.

Kronos Bio

Using small-molecule microarrays for new leads on traditionally undruggable proteins

The drug industry has a moniker for the kinds of proteins that Angela Koehler studies: undruggable. She hates the word.

The Massachusetts Institute of Technology chemist began studying transcription factors, a class of proteins that turn genes on and off, more than two decades ago. One particularly wily member, Myc, is overabundant in the majority of cancers. Although blocking Myc or reducing its levels could help slow tumor progression, drugmakers haven’t found a molecule that can do the job. To many, Myc is simply undruggable.

Koehler begs to differ. She thinks that because most scientists are trying to drug the protein in a purified form, they’re missing out on opportunities to block Myc in its natural environment, where it may assume a different shape or form complexes with other proteins. In fact, her lab has identified a compound that indirectly reduces active Myc levels by binding its partner protein.

Her preliminary experiments—still under review for publication—have already excited investors. In November 2017, biotech entrepreneur and Two River partner Arie Belldegrun helped Koehler found Kronos Bio. One year in, Kronos is off to an astounding start with $18 million in seed financing and a mission to drug traditionally undruggable cancer targets, including Myc.

Credit: Kronos Bio

Kronos uses small-molecule microarrays (SMMs) to find compounds that bind traditionally undruggable proteins. First, a fluorescent tag is attached to the target protein in a mixture of unfiltered proteins from a lysed cell. If the target protein, or other proteins attached to the target protein, binds a compound on the SMM, scientists can pinpoint the interaction thanks to the fluorescent tag and study that compound for further drug development.

Belldegrun helped recruit a high-profile scientist to lead the company as CEO: Norbert Bischofberger, the former vice president of R&D at Gilead Sciences.

The technology behind Kronos is a drug discovery tool that Koehler helped pioneer nearly 20 years ago: the small-molecule microarray. An SMM is a glass slide with thousands of unique compounds fixed to its surface. Whereas most companies test purified proteins, Kronos spreads the innards of cells over the slide wholesale in hopes of finding compounds that bind unpurified proteins—those in their natural state.

The technique was essential for Koehler’s Myc discovery. “When it is purified from a cell, Myc is intrinsically disordered. It is essentially a piece of spaghetti,” she says, which leaves it ill suited for inhibition by small molecules. Furthermore, Myc doesn’t do much on its own. It’s active, and thus problematic, only when it binds to a partner protein called Max—an event that looks like the transformation of a limp noodle into a comparatively rigid rotini. By using SMMs, Koehler discovered a compound that stabilizes Max-Max pairs, leaving little leftover Max for the cancer-promoting Myc-Max pairs.

Although SMMs are not new, Bischofberger was surprised to learn that the drug industry has been slow to adopt them. Kronos is using them to cast a wide net while searching for compounds that bind proteins. For instance, a compound may bind the target protein alone or while the protein is attached to a larger complex. “We can be agnostic as to how the target protein exists,” Bischofberger says.

Koehler’s lab has also used SMMs to find compounds that block another tough-to-target transcription factor: a mutant, drug-resistant version of the androgen receptor AR-V7, which drives prostate cancer.

Yet another Kronos strategy for tackling stubborn proteins is targeted protein degradation (see 10 Start-Ups member Kymera Therapeutics). This experimental approach uses small molecules that bind a target protein at one end and a protein called a ubiquitin E3 ligase at the other. The ligase tags the target protein for destruction. More than 600 ligases are known, but most biotech firms are focused on only three. Kronos is deploying SMMs to find compounds that bind new ligases, found only in a specific tissue or cell type, to minimize side effects. Those ligase-binding molecules will then be linked to compounds that bind several undisclosed cancer target proteins.

Bischofberger, who spent nearly 30 years molding Gilead into the antiviral and cancer therapy leader it is today, relishes the opportunity to build a small company again. “It’s too early to retire,” the 62-year-old says. “I was longing to repeat the Gilead experience one more time.”

Kymera Therapeutics

Cambridge, Mass.-based biotech is writing the rules for protein degradation﻿

A few years ago, Nello Mainolfi, a medicinal chemist who loves a challenge, became enchanted with an emerging field of drug discovery called targeted protein degradation. Rather than simply block the activity of bad-behaving proteins, protein degradation uses complex small molecules to tag them for the cell’s trash bin.

The degrader molecules feature one end that binds to a target protein and another that grasps a ligand to, through a series of steps, tag it for destruction in the proteasome. Though the molecules look odd and unwieldy, the concept was tantalizing.

By 2015, academic researchers were showing that protein degraders could potently and swiftly lower protein levels in cells. Moreover, because the degraders need only a toehold on a protein to do their work, targets that had long been inaccessible to drug companies—the majority of the human proteome, it turns out—suddenly seemed up for grabs.

Credit: Kymera Therapeutics

Kymera's protein degraders are heterobifunctional small molecules that hijack the natural protein-disposal process. The compounds force a disease-causing protein to nestle up alongside an E3 ubiquitin ligase (1), which recruits an E2 protein and tags the targeted protein for ubiquitination (2) and subsequent breakdown into amino acids in the proteasome (3).

But Mainolfi saw a problem. At the time, most of the promising protein degraders were found empirically—researchers could make compounds that broke down proteins, but relied on guesswork when tweaking those molecules to behave like a drug. If chemists were going to make a dent in the vast landscape of undruggable proteins, they would need a more systematic approach to developing these molecules. Someone would have to write the rules for the technology.

In early 2016, Kymera Therapeutics was born to do that. Incubated by Atlas Venture, Kymera set out to rationally design protein degraders and turn them into drugs. Once established, such a design platform “could allow us to have access to therapeutic questions people haven’t been able to ask in the past 150 years of drug discovery and development,” says Mainolfi, now the firm’s chief technology officer.

Establishing those rules is proving no small feat. Kymera’s team has spent the past two years trying to answer a few key questions. For example, of the 80% of the human proteome that conventional small molecules can’t access, what portion has footholds for protein degraders? And once researchers create a degrader that works in cells, is there a way to predict how it will behave in humans? Moreover, the company has devoted much energy to exploring new E3 ligases and binders—the end of the bifunctional molecule that kick-starts the process of tagging the protein for the trash.

In April, Kymera unveiled a partnership with GlaxoSmithKline intended to work on the first question. The companies have been putting a series of undruggable proteins through tests to look for hits. The effort has yielded “a more sophisticated understanding of the types of proteins that can be liganded,” Mainolfi says.

Kymera has also spent a lot of time and money to understand the kinetics of protein degradation. Protein levels are constantly in flux in a cell, even without the presence of a degrader, making it tough to develop biomarkers, or tests, to assess the efficacy of a drug in humans. “What’s missing in this space is the complexity of in vivo kinetics,” Mainolfi says, adding that Kymera’s first publication will explore this topic.

That deep exploration has helped the firm make quick progress toward the clinic. Kymera plans to start human tests of its lead compound in January 2020, just over two years after the company closed its first major round of financing, CEO Laurent Audoly says.

By then, other protein degraders will likely have made it into humans. Arvinas, which spun out of the lab of Yale University chemical biologist Craig Crews in 2013, expects to start clinical trials of two degraders next year. Several other biotech firms—including C4 Therapeutics, Vividion Therapeutics, and Sitryx—have attracted major funding to push the technology forward. And big pharma firms like Novartis have sizable internal efforts.

Competition is fierce, but Audoly says Kymera is in it for the long haul. The company plans to take its drug candidate to the clinic itself and is “building a business that will be around for decades,” he says.

At a glance

Funding or notable partners: $50 million from industrial partners and venture capitalists

When he was young, Ajikumar Parayil worked with his family on a farm in India growing ginger, pepper, turmeric, and other spices. The enterprise was risky, he recalls. “There have been times when a single fungal infection has wiped out an entire crop.”

Now, Parayil is CEO and cofounder of Manus Bio, a start-up working to engineer microbes to replicate how plants manufacture natural chemical compounds. Its goal is to make such compounds accessible, affordable, and immune to the vagaries of weather and plant disease.

“Plants are the most amazing chemists,” Parayil says. “They are able to create and produce a large and diverse set of chemicals which are integrated into many of the products used in our daily lives, from the time we wake up in the morning to when we go to bed.”

Credit: C&EN/Shutterstock

By reengineering microbes to synthesize plant chemicals, Manus Bio hopes to improve the efficiency and cost-effectiveness of chemical manufacturing. The engineered microbes are scaled up via a fermentation process, leading to final products such as pharmaceuticals and fragrances.

Parayil and Gregory Stephanopoulos, professor of chemical engineering at Massachusetts Institute of Technology, developed Manus Bio’s core technology while Parayil was a postdoc in Stephanopoulos’s lab in 2010. As his postdoc was wrapping up, he began looking for academic positions, but it was also clear to him that “if you can replace plant processes with fermentation processes, that’s going to have a real impact on society.”

“With fermentation, you can perform biology and chemistry in a microbe in well-controlled environments and produce your product anywhere in the world,” Parayil says. Stephanopoulos agreed. He notes that by using microbes rather than plants for important compounds, “you can free up land for the production of useful foods.”

Parayil enrolled in a number of entrepreneurial courses at MIT to learn how to put together a business strategy and raise funding to commercialize his technology. “I went to the MIT Sloan School of Management and started talking to people about the technology and its potential,” he says. “We spent over a year developing the concept into a solid business plan.” Manus Bio launched operations in 2012.

If you can replace plant processes with fermentation processes, that’s going to have a real impact on society.

Ajikumar Parayil, cofounder and CEO, Manus Bio

Instead of a bottom-up combinatorial DNA-engineering approach, Manus Bio takes a top-down data- and insight-driven approach. “We have a strong ‘omics’ platform where we apply metabolomics, proteomics, and transcriptomics to understand the biology of the engineered microbe and then use that information for engineering the next generation of microbial strains,” Parayil says.

Manus Bio says its scientists can use the miniature microbial factories to produce thousands of natural compounds found in everyday products, including cosmetics, fragrances, pharmaceuticals, and agricultural chemicals.

In one project, with the Bill & Melinda Gates Foundation, Manus Bio is producing artemisinic acid, a precursor to the antimalarial drug artemisinin. Another project involves engineering microbes to produce a rare and high-performing sweetener molecule from the stevia plant, called Reb M.

Manus Bio has raised $50 million in funding from industrial partners and venture capitalists. The company has purchased a manufacturing plant in Augusta, Ga., and plans to launch its first fermentation product early next year; it has several more in the pipeline. It has 35 employees and plans to grow to 60 over the next couple of years, with most of the new positions on the manufacturing side.

“This new biotechnological process for next-generation chemical manufacturing is going to revolutionize people’s lives,” Parayil says. “I used to extract latex from rubber plants while I was growing up in India. Now, we can deploy our technology to make isoprene or natural rubber without being reliant on plants and destroying prime land which can be used for food production. That’s the power of engineering chemistry using biology.”

For making short DNA strands, the phosphoramidite chemistry invented and commercialized in the 1980s is hard to beat. But the method peters out after about 100 nucleotides. Applications such as synthetic biology and data storage will require longer strands than that.

“If all the world needed was 20-mers or 30-mers, phosphoramidite chemistry really excels at those,” says J. William Efcavitch, who was involved in the commercialization of phosphoramidite-based DNA synthesis. “But we’re looking for longer oligonucleotides or modified oligonucleotides that are difficult, if not impossible, for the phosphoramidite chemistry.”

That “we” refers to Molecular Assemblies, a San Diego-based company that hopes to use enzymes to circumvent the problems of phosphoramidite-based DNA synthesis. Efcavitch cofounded the firm in 2013 and serves as its chief scientific officer.

Credit: C&EN/Shutterstock

Molecular Assemblies uses a template-independent enzyme (TdT) to synthesize long DNA strands. In each cycle, a nucleotide with an attached terminator is added to the growing strand, the reactants are rinsed away, and the terminator is removed. Then the cycle is repeated.

Molecular Assemblies is not alone in wanting to make long pieces of DNA. For example, the start-up Twist Bioscience stitches together pieces made by silicon-based phosphoramidite synthesis into long DNA strands. But Molecular Assemblies wants to get away from that chemistry altogether.

“Phosphoramidite DNA synthesis technology has reached a technological plateau,” Efcavitch says. “A combination of factors led us to explore enzymatic synthesis not as a replacement for but as a supplement to phosphoramidite chemistry.” In addition to the length limits, the older chemistry requires significant postsynthesis processing and produces hazardous waste, including acids, bases, and organic solvents.

The enzyme that Molecular Assemblies uses is called terminal deoxynucleotidyl transferase, or TdT. It’s the only known DNA-synthesizing enzyme that doesn’t require a template. It just randomly adds nucleotides to the ends of DNA strands. Controversy raged for decades over its natural role, Efcavitch notes.

“TdT is a very efficient enzyme,” he says. If given nucleotides without a terminator, it will perform random polymerization with whatever it can grab hold of, he says. “We’ve made single-stranded DNA that is close to 1,000 nucleotides long.”

But such lengths are currently possible only with random sequences or repeating stretches of one nucleotide. To get specific sequences, Molecular Assemblies scientists have to control the enzyme. They achieve such control by attaching reversible terminators to the nucleotides and adding new nucleotides one at a time.

In the company’s method, an initiator is tethered to a solid support over which the enzyme and desired nucleotide are flowed as reagents. The reversible terminator ensures that only one nucleotide is added to the growing DNA strand in each reaction cycle. After the addition step, the firm chemically stops the reaction, rinses, removes the terminator, and repeats the whole cycle until it’s made the desired sequence.

So far, the company has focused on optimizing the two chemical steps: the addition of the nucleotide and the removal of the terminator. To get the kinds of lengths it wants, those reactions need yields greater than 99.9%.

The company is eyeing multiple applications for its long DNA strands, but topping the list are synthetic biology and data storage. “Our market entry point is oligonucleotides that are 150 nucleotides long,” Efcavitch says. “The holy grail would be to make a gene-size fragment of 1,500 nucleotides.” In August, the company announced that it had used its synthesis method to store a text message, which it retrieved with DNA sequencing.

The company has so far raised about $7 million from a variety of investors. “We have a nice balance of investors so far,” CEO Michael Kamdar says. “We have some folks who are investors because they have an interest in the synthetic biology and life science applications. Then we have others who have interest in the data and information storage applications.”

RNAgri

Making RNA interference practical for precise pest control

At a glance

Focus: High-volume production of RNA for RNA interference applications

Technology: Fermentation route with modified microbes

Founder: Juan Arhancet

Funding or notable partners: Research partnership with Monsanto and $3.2 million in seed funding from Missouri Technology, BioGenerator, and Yield Lab﻿

It has been 20 years since scientists discovered that short strands of RNA can turn off specific genes inside an organism. Almost immediately, they attempted to harness the technique, called RNA interference, or RNAi, to prevent the production of problematic proteins in people. After a bevy of technical challenges, the U.S. Food & Drug Administration finally approved the first-ever RNAi therapy in August.

In the agricultural wing of the life sciences, researchers use RNAi as a tool to study the function of plant genes by silencing them. Now, the St. Louis-based start-up RNAgri has a more audacious goal: Kill crop-munching insects with RNA that prevents the production of vital proteins while leaving beneficial insects intact.

Large agriculture companies have long sought to use RNAi as more than a research tool, but turning it into a product did not seem feasible, says RNAgri CEO John Killmer. For one thing, the high cost of synthesizing RNA made it impractical to apply to fields. What’s more, when RNA gets into an organism’s cell, it is quickly degraded by enzymes.

Credit: RNAgri/C&EN

RNAgri produces double-stranded RNA via fermentation with modified microbes. First, plasmids alter the microbes so that they produce RNA that can interfere with the production of specific proteins in a target species, such as the Colorado potato beetle. Then the microbes produce the desired double-stranded RNA as well as protein capsids that protect the RNA from degradation enzymes in the target species. The fermentation process enables the scale-up of RNA interference (RNAi) treatments at a low cost, making it possible to use RNAi instead of chemical pesticides to control crop pests.

RNAgri was founded in 2011 by serial entrepreneur and Monsanto veteran Juan Arhancet. Then called Apse, the firm first focused on protein purification before moving into making RNA in 2013. Arhancet is now leading another RNA-focused start-up.

Killmer, also a veteran of Monsanto, took the reins in 2015. He says the company has developed a technique to make RNA at scale and protect it from degradation by RNA-chopping enzymes. Its scientists produce RNA via fermentation using engineered microbes. Those microbes also produce proteins that fully or partially surround the RNA and protect it until it can reach its target.

We are very confident we have the lowest-cost process for producing RNA.

John Killmer, CEO, RNAgri

Those targets are chosen specifically for each species of insect. According to Killmer, the company bases its RNA sequences on DNA that is unique to the intended victim and does not exist in beneficial predatory insects like ladybugs.

One target is the Colorado potato beetle, a voracious eater of potato, tomato, and pepper leaves that can be expensive and difficult to control. Killmer’s team found a unique sequence of potato beetle DNA, made the matching RNA, and sent it off to a testing company. “All of the potato beetles died, while the controls were fine, so we knew the test was right,” he reports. Subsequent tests showed that a tiny dose—equivalent to 2.5 g used on a hectare—was effective.

Because RNA is everywhere—in food and the environment—it’s an environmentally benign alternative to chemical pesticides, Killmer says. In the future, it could also provide a new way to alter traits inside plants without having to change their genome via genetic engineering or gene editing.

And in addition to agricultural pests, RNAgri anticipates a market for RNAi used against household pests like fire ants, termites, and cockroaches.

In April, RNAgri formed a research partnership with Monsanto to explore the RNA production technology in honeybee health and elsewhere in agriculture. The start-up has raised funds from angel investors and from three agriculture-focused start-up incubators. Killmer says the firm will look to raise its first venture capital round within the next year.

Killmer acknowledges that it has been a long road for RNAi, but he expects to see big agriculture firms make spray-on RNAi products soon. “We are very confident we have the lowest-cost process for producing RNA,” he says. “And we certainly will be on the radar screen for anyone that wants to have a product for broad-acre agriculture.”

Solugen

Challenging the 75-year-old process for making hydrogen peroxide

Solugen founders Sean Hunt (left) and Gaurab Chakrabarti take a break during AkzoNobel's chemistry innovation contest earlier this year in Sweden.

At a glance

Launched: 2016

Headquarters: Houston and Philadelphia

Focus: Hydrogen peroxide and other oxygen-containing chemicals

Technology: Enzyme-driven oxidation

Founders: Gaurab Chakrabarti and Sean Hunt

Funding or notable partners: $4.4 million in seed funding; undisclosed series A funding; development agreement with AkzoNobel﻿

For more than 75 years, the simple chemical hydrogen peroxide has been synthesized via one very complex route. Solugen wants to change that.

Solugen was launched in early 2016 by Sean Hunt and Gaurab Chakrabarti, scientists who at the time were both in their late 20s. Hunt was a recent Ph.D. graduate in chemical engineering from Massachusetts Institute of Technology; Chakrabarti was still completing an M.D.-Ph.D. at the University of Texas Southwestern Medical Center.

While researching pancreatic cancer, Chakrabarti discovered an enzyme that excels at oxidizing sugars into hydrogen peroxide and organic acids. Through a classmate, he met Hunt, who for his Ph.D. was developing a nanoparticle metal catalyst for producing hydrogen peroxide. Not surprisingly, they got along.

Hunt, steeped in heterogeneous catalysis, was initially skeptical of Chakrabarti’s discovery. “I never liked enzymes—I thought they were too fragile, too expensive,” Hunt recalls. But he became a convert when he saw how robust they are at reducing oxygen.

Credit: Solugen/C&EN/Shutterstock

Hydrogen peroxide has been made the same energy-intensive way for more than 75 years. Using an enzyme discovered by one of its founders, Solugen is commercializing a new, simpler method that turns oxygen and glucose into hydrogen peroxide and gluconic acid, a valuable coproduct.

The two decided to form a company that combined Chakrabarti’s enzyme, which he enhanced using CRISPR/Cas9 gene editing, with a reactor Hunt designed specifically for the oxidation process.

By April 2017, the partners had raised seed funding from investors, including Y Combinator, Refactor Capital, and MIT. They also did something unconventional for a chemistry start-up: They launched a line of plant-based cleaning wipes instilled with hydrogen peroxide and gluconic acid, the products of treating glucose with Chakrabarti’s enzyme.

The pair got some grief for applying cool chemistry to a gimmicky consumer product. But Chakrabarti says the foray into retail was calculated to get attention. “Going to big companies directly takes forever,” he says. “So we decided to start our own brand.”

The gambit seems to have worked. The wipes sold like hotcakes, and Solugen recently struck a deal to sell the product line to a large wipes manufacturer. The attention also helped get the firm a slot in AkzoNobel’s Imagine Chemistry start-up contest. It went on to win a joint development agreement with AkzoNobel, which happens to be one of the world’s largest producers of hydrogen peroxide by the conventional method.

That method, commercialized in the 1930s, is a five-step, energy-intensive process that uses an anthraquinone to control the reaction between hydrogen and oxygen. Direct synthesis, of course, would be preferred, but past attempts tended to yield water.

We like to put oxygen in places it doesn’t like to be.

Gaurab Chakrabarti, CEO, Solugen

As part of its due diligence, Hunt says, AkzoNobel evaluated the economics of the new process and found it compares favorably to the traditional route, in large part because it yields two valuable products from one simple raw material. Under their development agreement, Solugen and AkzoNobel are now working to perfect Hunt’s reactor.

Unlike many young start-ups, Solugen actually makes stuff. Today, at its pilot plant in Houston, Solugen is producing a mixture of hydrogen peroxide and gluconic acid at a rate of about 10 metric tons per month. The firm could separate it, but instead it’s using the mixture for the wipes and selling it to customers in the water treatment and oil and gas industries as a dual oxidant and corrosion inhibitor.

The founders are also pursuing other reactions. “We like to put oxygen in places it doesn’t like to be,” Chakrabarti says. Another potential product pair is hydrogen peroxide and acetic acid, which form peracetic acid. Aldehydes such as glutaraldehyde and acetaldehyde are also candidate coproducts.

Impressed by Solugen’s combination of current sales and broad future prospects, investors recently forked over a series A funding round of undisclosed size. The firm is hiring and intends to double its staff of 13 by the end of 2019. Chakrabarti and Hunt expect to keep busy for a while. “We were born to do this,” Hunt says. “We want to retire at Solugen 30 years from now.”

CORRECTION

This story was updated on Nov. 13, 2018, to correct the credit on the photo of Manus Bio's chief technology officer and cofounders.